├── .clang-format ├── .github ├── CONTRIBUTING.md ├── FUNDING.yml ├── ISSUE_TEMPLATE.md ├── PULL_REQUEST_TEMPLATE.md └── workflows │ └── testing.yml ├── .gitignore ├── .gitmodules ├── Jenkinsfile ├── LICENSE.md ├── README.md ├── RELEASE-NOTES.txt ├── lib └── rapidjson_1.1.0 │ └── rapidjson │ ├── allocators.h │ ├── cursorstreamwrapper.h │ ├── document.h │ ├── encodedstream.h │ ├── encodings.h │ ├── error │ ├── en.h │ └── error.h │ ├── filereadstream.h │ ├── filewritestream.h │ ├── fwd.h │ ├── internal │ ├── biginteger.h │ ├── diyfp.h │ ├── dtoa.h │ ├── ieee754.h │ ├── itoa.h │ ├── meta.h │ ├── pow10.h │ ├── regex.h │ ├── stack.h │ ├── strfunc.h │ ├── strtod.h │ └── swap.h │ ├── istreamwrapper.h │ ├── memorybuffer.h │ ├── memorystream.h │ ├── msinttypes │ ├── inttypes.h │ └── stdint.h │ ├── ostreamwrapper.h │ ├── pointer.h │ ├── prettywriter.h │ ├── rapidjson.h │ ├── reader.h │ ├── schema.h │ ├── stream.h │ ├── stringbuffer.h │ └── writer.h ├── licenses ├── README.txt └── stan-doc-license.txt ├── make ├── clang-tidy ├── cpplint ├── doxygen └── tests ├── makefile ├── runTests.py └── src ├── doxygen ├── doxygen-footer.html ├── doxygen.cfg ├── mainpage.dox ├── stan.dox ├── stanlogo-main.png └── std.dox ├── stan ├── analyze │ └── mcmc │ │ ├── autocovariance.hpp │ │ ├── check_chains.hpp │ │ ├── compute_effective_sample_size.hpp │ │ ├── compute_potential_scale_reduction.hpp │ │ ├── ess.hpp │ │ ├── mcse.hpp │ │ ├── rank_normalization.hpp │ │ ├── rhat.hpp │ │ ├── split_chains.hpp │ │ ├── split_rank_normalized_ess.hpp │ │ └── split_rank_normalized_rhat.hpp ├── callbacks │ ├── concurrent_writer.hpp │ ├── interrupt.hpp │ ├── json_writer.hpp │ ├── logger.hpp │ ├── stream_logger.hpp │ ├── stream_writer.hpp │ ├── structured_writer.hpp │ ├── tee_writer.hpp │ ├── unique_stream_writer.hpp │ └── writer.hpp ├── io │ ├── array_var_context.hpp │ ├── chained_var_context.hpp │ ├── deserializer.hpp │ ├── dump.hpp │ ├── empty_var_context.hpp │ ├── ends_with.hpp │ ├── json │ │ ├── json_data.hpp │ │ ├── json_data_handler.hpp │ │ ├── json_error.hpp │ │ ├── json_handler.hpp │ │ └── rapidjson_parser.hpp │ ├── random_var_context.hpp │ ├── serializer.hpp │ ├── stan_csv_reader.hpp │ ├── validate_dims.hpp │ ├── validate_zero_buf.hpp │ └── var_context.hpp ├── lang │ └── rethrow_located.hpp ├── mcmc │ ├── base_adaptation.hpp │ ├── base_adapter.hpp │ ├── base_mcmc.hpp │ ├── chains.hpp │ ├── chainset.hpp │ ├── covar_adaptation.hpp │ ├── fixed_param_sampler.hpp │ ├── hmc │ │ ├── base_hmc.hpp │ │ ├── hamiltonians │ │ │ ├── base_hamiltonian.hpp │ │ │ ├── dense_e_metric.hpp │ │ │ ├── dense_e_point.hpp │ │ │ ├── diag_e_metric.hpp │ │ │ ├── diag_e_point.hpp │ │ │ ├── ps_point.hpp │ │ │ ├── softabs_metric.hpp │ │ │ ├── softabs_point.hpp │ │ │ ├── unit_e_metric.hpp │ │ │ └── unit_e_point.hpp │ │ ├── integrators │ │ │ ├── base_integrator.hpp │ │ │ ├── base_leapfrog.hpp │ │ │ ├── expl_leapfrog.hpp │ │ │ └── impl_leapfrog.hpp │ │ ├── nuts │ │ │ ├── adapt_dense_e_nuts.hpp │ │ │ ├── adapt_diag_e_nuts.hpp │ │ │ ├── adapt_softabs_nuts.hpp │ │ │ ├── adapt_unit_e_nuts.hpp │ │ │ ├── base_nuts.hpp │ │ │ ├── dense_e_nuts.hpp │ │ │ ├── diag_e_nuts.hpp │ │ │ ├── softabs_nuts.hpp │ │ │ └── unit_e_nuts.hpp │ │ ├── nuts_classic │ │ │ ├── adapt_dense_e_nuts_classic.hpp │ │ │ ├── adapt_diag_e_nuts_classic.hpp │ │ │ ├── adapt_unit_e_nuts_classic.hpp │ │ │ ├── base_nuts_classic.hpp │ │ │ ├── dense_e_nuts_classic.hpp │ │ │ ├── diag_e_nuts_classic.hpp │ │ │ └── unit_e_nuts_classic.hpp │ │ ├── static │ │ │ ├── adapt_dense_e_static_hmc.hpp │ │ │ ├── adapt_diag_e_static_hmc.hpp │ │ │ ├── adapt_softabs_static_hmc.hpp │ │ │ ├── adapt_unit_e_static_hmc.hpp │ │ │ ├── base_static_hmc.hpp │ │ │ ├── dense_e_static_hmc.hpp │ │ │ ├── diag_e_static_hmc.hpp │ │ │ ├── softabs_static_hmc.hpp │ │ │ └── unit_e_static_hmc.hpp │ │ ├── static_uniform │ │ │ ├── adapt_dense_e_static_uniform.hpp │ │ │ ├── adapt_diag_e_static_uniform.hpp │ │ │ ├── adapt_softabs_static_uniform.hpp │ │ │ ├── adapt_unit_e_static_uniform.hpp │ │ │ ├── base_static_uniform.hpp │ │ │ ├── dense_e_static_uniform.hpp │ │ │ ├── diag_e_static_uniform.hpp │ │ │ ├── softabs_static_uniform.hpp │ │ │ └── unit_e_static_uniform.hpp │ │ └── xhmc │ │ │ ├── adapt_dense_e_xhmc.hpp │ │ │ ├── adapt_diag_e_xhmc.hpp │ │ │ ├── adapt_softabs_xhmc.hpp │ │ │ ├── adapt_unit_e_xhmc.hpp │ │ │ ├── base_xhmc.hpp │ │ │ ├── dense_e_xhmc.hpp │ │ │ ├── diag_e_xhmc.hpp │ │ │ ├── softabs_xhmc.hpp │ │ │ └── unit_e_xhmc.hpp │ ├── sample.hpp │ ├── stepsize_adaptation.hpp │ ├── stepsize_adapter.hpp │ ├── stepsize_covar_adapter.hpp │ ├── stepsize_var_adapter.hpp │ ├── var_adaptation.hpp │ └── windowed_adaptation.hpp ├── model │ ├── finite_diff_grad.hpp │ ├── grad_hess_log_prob.hpp │ ├── grad_tr_mat_times_hessian.hpp │ ├── gradient.hpp │ ├── gradient_dot_vector.hpp │ ├── hessian.hpp │ ├── hessian_times_vector.hpp │ ├── indexing.hpp │ ├── indexing │ │ ├── access_helpers.hpp │ │ ├── assign.hpp │ │ ├── assign_cl.hpp │ │ ├── assign_varmat.hpp │ │ ├── deep_copy.hpp │ │ ├── index.hpp │ │ ├── rvalue.hpp │ │ ├── rvalue_at.hpp │ │ ├── rvalue_cl.hpp │ │ ├── rvalue_index_size.hpp │ │ └── rvalue_varmat.hpp │ ├── log_prob_grad.hpp │ ├── log_prob_propto.hpp │ ├── model_base.hpp │ ├── model_base_crtp.hpp │ ├── model_functional.hpp │ ├── model_header.hpp │ ├── prob_grad.hpp │ ├── rethrow_located.hpp │ └── test_gradients.hpp ├── optimization │ ├── bfgs.hpp │ ├── bfgs_linesearch.hpp │ ├── bfgs_update.hpp │ ├── lbfgs_update.hpp │ └── newton.hpp ├── services │ ├── diagnose │ │ ├── defaults.hpp │ │ └── diagnose.hpp │ ├── error_codes.hpp │ ├── experimental │ │ └── advi │ │ │ ├── defaults.hpp │ │ │ ├── fullrank.hpp │ │ │ └── meanfield.hpp │ ├── optimize │ │ ├── bfgs.hpp │ │ ├── defaults.hpp │ │ ├── laplace_sample.hpp │ │ ├── lbfgs.hpp │ │ └── newton.hpp │ ├── pathfinder │ │ ├── multi.hpp │ │ ├── psis.hpp │ │ └── single.hpp │ ├── sample │ │ ├── defaults.hpp │ │ ├── fixed_param.hpp │ │ ├── hmc_nuts_dense_e.hpp │ │ ├── hmc_nuts_dense_e_adapt.hpp │ │ ├── hmc_nuts_diag_e.hpp │ │ ├── hmc_nuts_diag_e_adapt.hpp │ │ ├── hmc_nuts_unit_e.hpp │ │ ├── hmc_nuts_unit_e_adapt.hpp │ │ ├── hmc_static_dense_e.hpp │ │ ├── hmc_static_dense_e_adapt.hpp │ │ ├── hmc_static_diag_e.hpp │ │ ├── hmc_static_diag_e_adapt.hpp │ │ ├── hmc_static_unit_e.hpp │ │ ├── hmc_static_unit_e_adapt.hpp │ │ └── standalone_gqs.hpp │ └── util │ │ ├── create_rng.hpp │ │ ├── create_unit_e_dense_inv_metric.hpp │ │ ├── create_unit_e_diag_inv_metric.hpp │ │ ├── duration_diff.hpp │ │ ├── experimental_message.hpp │ │ ├── generate_transitions.hpp │ │ ├── gq_writer.hpp │ │ ├── initialize.hpp │ │ ├── inv_metric.hpp │ │ ├── mcmc_writer.hpp │ │ ├── read_dense_inv_metric.hpp │ │ ├── read_diag_inv_metric.hpp │ │ ├── run_adaptive_sampler.hpp │ │ ├── run_sampler.hpp │ │ ├── validate_dense_inv_metric.hpp │ │ └── validate_diag_inv_metric.hpp ├── variational │ ├── advi.hpp │ ├── base_family.hpp │ ├── families │ │ ├── normal_fullrank.hpp │ │ └── normal_meanfield.hpp │ └── print_progress.hpp └── version.hpp └── test ├── integration ├── compile_models_test.cpp ├── compile_standalone_functions_test.cpp ├── mtu │ ├── mcmc.cpp │ └── model.cpp ├── multiple_translation_units_test.cpp └── standalone_functions_test.cpp ├── test-models ├── README.txt ├── expressions │ └── simple_udf.stan ├── good-standalone-functions │ ├── basic.stanfuncs │ ├── integrate.stanfuncs │ ├── lgamma.stanfuncs │ └── special_functions.stanfuncs ├── good │ ├── mcmc │ │ └── hmc │ │ │ ├── common │ │ │ ├── gauss.stan │ │ │ └── gauss3D.stan │ │ │ ├── hamiltonians │ │ │ └── funnel.stan │ │ │ └── integrators │ │ │ ├── command.stan │ │ │ └── gauss.stan │ ├── model │ │ ├── accumulate.stan │ │ ├── parameters.inits.json │ │ ├── parameters.stan │ │ └── valid.stan │ ├── optimization │ │ ├── constrain_sigma.stan │ │ ├── exponential_boundary.stan │ │ ├── rosenbrock.stan │ │ └── simple_jacobian.stan │ ├── services │ │ ├── bernoulli.data.json │ │ ├── bernoulli.stan │ │ ├── bernoulli_fit.csv │ │ ├── bug_2390_fitted_params.csv │ │ ├── bug_2390_gq.stan │ │ ├── bug_2390_model.stan │ │ ├── eight_schools.stan │ │ ├── gq_test_multidim.stan │ │ ├── gq_test_multidim_fit.csv │ │ ├── gq_test_zero_sized.stan │ │ ├── multi_normal.stan │ │ ├── normal_glm.stan │ │ ├── test_fail.stan │ │ ├── test_gq.stan │ │ ├── test_gq2.stan │ │ ├── test_lp.stan │ │ └── zero_params.stan │ └── variational │ │ ├── eta_should_be_big.stan │ │ ├── eta_should_be_small.stan │ │ ├── eta_should_fail.stan │ │ ├── gradient_warn.data.json │ │ ├── gradient_warn.stan │ │ ├── hier_logistic.data.json │ │ ├── hier_logistic.stan │ │ ├── hier_logistic_cp.stan │ │ ├── multivariate_no_constraint.stan │ │ ├── multivariate_with_constraint.stan │ │ ├── univariate_no_constraint.stan │ │ └── univariate_with_constraint.stan ├── included │ ├── badrecurse1.stan │ ├── badrecurse2.stan │ ├── badrecurse3.stan │ ├── incl_fun.stan │ ├── incl_nested.stan │ ├── incl_params.stan │ ├── incl_rec.stan │ └── simple1.stan └── performance │ ├── logistic.data.json │ └── logistic.stan └── unit ├── analyze └── mcmc │ ├── ar1.csv │ ├── autocovariance_test.cpp │ ├── check_chains_test.cpp │ ├── compute_effective_sample_size_test.cpp │ ├── compute_potential_scale_reduction_test.cpp │ ├── ess_basic_test.cpp │ ├── mcse_test.cpp │ ├── rank_normalization_test.cpp │ ├── rhat_basic_test.cpp │ ├── split_chains_test.cpp │ ├── split_rank_normalized_ess_test.cpp │ ├── split_rank_normalized_rhat_test.cpp │ └── test_csv_files │ ├── bern1.csv │ ├── bern2.csv │ ├── bern3.csv │ ├── bern4.csv │ └── cmdstan-2-35-0-stansummary.csv ├── callbacks ├── interrupt_test.cpp ├── json_writer_test.cpp ├── logger_test.cpp ├── stream_logger_test.cpp ├── stream_writer_test.cpp ├── tee_writer_test.cpp ├── unique_stream_writer_test.cpp └── writer_test.cpp ├── expressions └── simple_udf_test.cpp ├── io ├── array_var_context_test.cpp ├── chained_var_context_test.cpp ├── deserializer_free_test.cpp ├── deserializer_stdvector_test.cpp ├── deserializer_test.cpp ├── deserializer_var_test.cpp ├── deserializer_varmat_test.cpp ├── dump_test.cpp ├── empty_var_context_test.cpp ├── ends_with_test.cpp ├── json │ ├── json_data_handler_test.cpp │ ├── json_data_test.cpp │ ├── json_data_tuples_test.cpp │ ├── json_ill_formed_test.cpp │ ├── json_parser_test.cpp │ └── util.hpp ├── random_var_context_test.cpp ├── serializer_stdvector_test.cpp ├── serializer_test.cpp ├── serializer_varmat_test.cpp ├── stan_csv_reader_test.cpp ├── test_csv_files │ ├── adaptation1.csv │ ├── bernoulli_no_samples.csv │ ├── bernoulli_thin.csv │ ├── bernoulli_variational.csv │ ├── bernoulli_warmup.csv │ ├── blocker.0.csv │ ├── eight_schools.csv │ ├── fixed_param_output.csv │ ├── header1.csv │ ├── header2.csv │ ├── header3.csv │ ├── metadata1.csv │ ├── metadata3.csv │ ├── no_parameters_hmc.csv │ └── samples1.csv ├── test_json_files │ ├── array_tuple_multi.json │ ├── arrays.json │ ├── d1_array_tuple_1d_real.json │ ├── d1_array_tuple_1d_tuple.json │ ├── d2_array_tuple_1d_real.json │ ├── inconsistent_array_tuples_1.json │ ├── inconsistent_array_tuples_2.json │ ├── inconsistent_array_tuples_3.json │ ├── inconsistent_array_tuples_4.json │ ├── not_stan_varname.json │ ├── redefine_vars_1.json │ ├── redefine_vars_2.json │ ├── redefine_vars_3.json │ ├── redefine_vars_4.json │ ├── redefine_vars_5.json │ ├── redefine_vars_6.json │ ├── tuple_arr_tuple.json │ ├── tuple_array_3d_2d.json │ ├── tuple_int_real.json │ ├── tuple_nested.json │ └── vars_plus_comments.json └── validate_zero_buf_test.cpp ├── mcmc ├── base_adapter_test.cpp ├── chains_test.cpp ├── chainset_test.cpp ├── covar_adaptation_test.cpp ├── hmc │ ├── base_hmc_test.cpp │ ├── hamiltonians │ │ ├── base_hamiltonian_test.cpp │ │ ├── dense_e_metric_test.cpp │ │ ├── diag_e_metric_test.cpp │ │ ├── ps_point_test.cpp │ │ ├── softabs_metric_test.cpp │ │ └── unit_e_metric_test.cpp │ ├── integrators │ │ ├── expl_leapfrog2_test.cpp │ │ ├── expl_leapfrog_test.cpp │ │ ├── impl_leapfrog2_test.cpp │ │ └── impl_leapfrog_test.cpp │ ├── mock_hmc.hpp │ ├── nuts │ │ ├── base_nuts_test.cpp │ │ ├── derived_nuts_test.cpp │ │ ├── instantiation_test.cpp │ │ ├── softabs_nuts_test.cpp │ │ └── unit_e_nuts_test.cpp │ ├── nuts_classic │ │ ├── base_nuts_classic_test.cpp │ │ ├── derived_nuts_classic_test.cpp │ │ └── instantiation_test.cpp │ ├── static │ │ └── base_static_hmc_test.cpp │ ├── static_uniform │ │ ├── base_static_uniform_test.cpp │ │ └── derived_static_uniform_test.cpp │ └── xhmc │ │ ├── base_xhmc_test.cpp │ │ ├── softabs_xhmc_test.cpp │ │ └── unit_e_xhmc_test.cpp ├── sample_test.cpp ├── stepsize_adaptation_test.cpp ├── test_csv_files │ ├── bernoulli_500.csv │ ├── bernoulli_default.csv │ ├── bernoulli_thin.csv │ ├── bernoulli_warmup.csv │ ├── blocker.1.csv │ ├── blocker.2.csv │ ├── datagen_output.csv │ ├── eight_schools_1.csv │ ├── eight_schools_2.csv │ ├── epil.1.csv │ └── epil.2.csv ├── var_adaptation_test.cpp └── windowed_adaptation_test.cpp ├── model ├── array_functions_roundtrip_test.cpp ├── compile_test.cpp ├── finite_diff_grad_test.cpp ├── grad_hess_log_prob_test.cpp ├── grad_tr_mat_times_hessian_test.cpp ├── gradient_dot_vector_test.cpp ├── gradient_test.cpp ├── hessian_test.cpp ├── hessian_times_vector_test.cpp ├── indexing │ ├── assign_cl_test.cpp │ ├── assign_test.cpp │ ├── assign_varmat_test.cpp │ ├── deep_copy_test.cpp │ ├── index_test.cpp │ ├── rvalue_cl_test.cpp │ ├── rvalue_index_size_test.cpp │ ├── rvalue_test.cpp │ ├── rvalue_varmat_test.cpp │ ├── util.hpp │ └── util_cl.hpp ├── log_prob_grad_test.cpp ├── log_prob_propto_test.cpp ├── model_base_crtp_test.cpp ├── model_base_test.cpp ├── model_functional_test.cpp ├── test_gradients_test.cpp └── test_model.hpp ├── optimization ├── bfgs_exponential_boundary_test.cpp ├── bfgs_linesearch_test.cpp ├── bfgs_minimizer_test.cpp ├── bfgs_test.cpp ├── bfgs_update_test.cpp └── lbfgs_update_test.cpp ├── rethrow_located_test.cpp ├── services ├── check_adaptation.hpp ├── diagnose │ ├── defaults_test.cpp │ └── diagnose_test.cpp ├── experimental │ └── advi │ │ ├── defaults_test.cpp │ │ ├── fullrank_test.cpp │ │ └── meanfield_test.cpp ├── instrumented_callbacks.hpp ├── optimize │ ├── bfgs_jacobian_test.cpp │ ├── bfgs_test.cpp │ ├── defaults_test.cpp │ ├── laplace_jacobian_test.cpp │ ├── laplace_sample_test.cpp │ ├── lbfgs_jacobian_test.cpp │ ├── lbfgs_test.cpp │ ├── newton_jacobian_test.cpp │ └── newton_test.cpp ├── pathfinder │ ├── eight_schools_test.cpp │ ├── normal_glm_test.cpp │ ├── normal_glm_test.json │ ├── psis_test.cpp │ └── util.hpp ├── sample │ ├── defaults_test.cpp │ ├── fixed_param_parallel_test.cpp │ ├── fixed_param_test.cpp │ ├── hmc_nuts_dense_e_adapt_no_params_test.cpp │ ├── hmc_nuts_dense_e_adapt_parallel_match_test.cpp │ ├── hmc_nuts_dense_e_adapt_parallel_test.cpp │ ├── hmc_nuts_dense_e_adapt_test.cpp │ ├── hmc_nuts_dense_e_parallel_test.cpp │ ├── hmc_nuts_dense_e_test.cpp │ ├── hmc_nuts_dense_inv_metric_test.cpp │ ├── hmc_nuts_diag_e_adapt_parallel_match_test.cpp │ ├── hmc_nuts_diag_e_adapt_parallel_test.cpp │ ├── hmc_nuts_diag_e_adapt_test.cpp │ ├── hmc_nuts_diag_e_parallel_test.cpp │ ├── hmc_nuts_diag_e_test.cpp │ ├── hmc_nuts_diag_inv_metric_test.cpp │ ├── hmc_nuts_unit_e_adapt_parallel_test.cpp │ ├── hmc_nuts_unit_e_adapt_test.cpp │ ├── hmc_nuts_unit_e_parallel_test.cpp │ ├── hmc_nuts_unit_e_test.cpp │ ├── hmc_static_dense_e_adapt_test.cpp │ ├── hmc_static_dense_e_test.cpp │ ├── hmc_static_dense_inv_metric_test.cpp │ ├── hmc_static_diag_e_adapt_test.cpp │ ├── hmc_static_diag_e_test.cpp │ ├── hmc_static_diag_inv_metric_test.cpp │ ├── hmc_static_unit_e_adapt_test.cpp │ ├── standalone_gqs_2390_test.cpp │ ├── standalone_gqs_bad_test.cpp │ ├── standalone_gqs_multidim_test.cpp │ ├── standalone_gqs_parallel_test.cpp │ ├── standalone_gqs_test.cpp │ └── standalone_gqs_zero_sized_test.cpp ├── util.hpp └── util │ ├── create_rng_test.cpp │ ├── experimental_message_test.cpp │ ├── fail_init_test.cpp │ ├── 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